Utilizing the analytical solution of the steady state sharp interface saltwater intrusion model in coastal aquifers, a multi-objective optimization formulation of pumping rates and well locations in a coastal aquifer is formulated to solve problems in water management practice. The proposed optimization problem uses progressive genetic algorithm technique and the method developed is applied to the previous work of Cheng et al. [2000]. Through this analysis, several other applications are provided to demonstrate the use of the model in practical applications. This work is the first to optimize pumping rates as well as well locations simultaneously in coastal aquifer management. Known the limitation of the analytical solution, the work is expanded to cover the physics of saltwater intrusion in a more realistic way. This is variable density flow in a variably saturated porous medium. In this method, mixing between two fluids such as saltwater and freshwater can be described and the porous medium is also expanded to cover saturated and unsaturated zones together. One of the objectives is to develop a three dimensional physical model, verify the model, and apply to various applications in coastal aquifers. The developed model, TechFlow, is used to investigate instability issues associated with the numerical solution of the Elder problem in the perspective that includes physical instability issues associated with density differences used in numerical solutions, sensitivity of the solution to idealization irregularity, and the importance of accurate estimation of the velocity field and its association to the grid density levels that is necessary to solve the problem accurately. Saltwater intrusion hydrodynamics in a beach under the influence of tidal effects is also investigated using TechFlow. Based on the results of TechFlow with the use of various boundary conditions for the transport equation, the saltwater intrusion hydrodynamics in a beach under the influence of tidal effects shows unique dynamics. These solutions are primarily affected by density differences, tidal effects on a mild slope, variably saturated porous medium and finite domain solution condition. TechFlow is also used to investigate saltwater upconing beneath pumping wells both two- and three-dimensional applications.